Embryonic stem cell (ESC) differentiation is a potentially powerful approach for generating a renewable source of cells for regenerative medicine. It is known that the microenvironment greatly influences ESC differentiation and self-renewal. Most biological studies have aimed in identifying individual molecules and signals. However, it is becoming increasingly accepted that the wide array of signals in the ESC microenvironment interact in a synergistic and antagonistic manner based on their temporal and spatial expression, dosage, and specific combinations. This interplay of microenvironmental factors regulates the ESC fate decisions to proliferate, self-renew, differentiate, and migrate. Despite this complexity, the study of stem cell cues in a systematic manner is technologically challenging, expensive, slow, and labor intensive. Here we propose to develop an enabling technology based on a high-throughput microfluidic system that overcomes many of these challenges. By providing a way of testing combinatorial microenvironments for directing stem cell differentiation, this approach promises to be of great benefit for tissue engineering.